Input Data FormatBioModule can read network files written in the following formats:
- Tab Delimited Format(TDF)
- PSI MI XML Format
A line of a TDF file stands for a protein-protein interaction(PPI), and each element of a PPI is separated from the next by a tab stop character; the first two elements are the interactors, and third one is the confidence score. The range of a confidence score should be between 0 and 1, and when it is not shown in a line of a TDF file, that means confidence score of the corresponding PPI equals to 1. A toy example is shown as follows:
protein_A protein_C 0.8
The PSI MI is a shortened form of "Proteomics Standards Initiative Molecular Interaction." It describes PPIs and associated data in XML format. The format specification of PSI MI 2.5 is available at: http://psidev.info/node/60.